Aim: The interdependencies between trophic interactions, environmental factors and anthropogenic forcing determine how species distributions change over time. Large changes in species distributions have occurred as a result of climate change. The objective of this study was to analyse how the spatial distribution of cod and flounder have changed in the Baltic Sea during the past four decades characterized by large hydrological changes. Location: Baltic Sea Taxon: Cod (Gadus morhua) and flounder (Platichthys flesus) Methods: Catch per unit of effort (CPUE) data for adult and juvenile cod and for adult flounder were modelled using Delta-Generalized additive models including environmental and geographical variables between 1979 and 2016. From the annual CPUE predictions for each species, yearly distribution maps and depth distribution curves were obtained. Mean depth and the depth range were estimated to provide an indication on preferred depth and habitat occupancy. Results: Adult and juvenile cod showed a contraction in their distribution in the southern areas of the Baltic Sea. Flounder, instead, showed an expansion in its distribution with an increase in abundance in the northern areas. The depth distributions showed a progressive shift of the mean depth of occurrence towards shallower waters for adult cod and flounder and towards deeper waters for juvenile cod, as well as a contraction of the species depth ranges, evident mainly from the late 1980s. Main conclusions: Our study illustrates large changes in the spatial distribution of cod and flounder in the Baltic Sea. The changes in depth distribution occurred from the late 1980s are probably due to a combination of expanded areas of hypoxia in deep waters and an increase in predation risk in shallow waters. The net effect of these changes is an increased spatial overlap between life stages and species, which may amplify cod cannibalism and the interaction strength between cod and flounder. Data_cod_flounderAdult cod, juvenile cod and flounder CPUE data (in grams). The datasets contain also the associated bottom temperature, salinity and oxygen concentration of each haul as well as the latitude and longitude in decimal degrees.
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doi: 10.14284/601
European Seabirds At Sea (ESAS) assembles offshore monitoring data on seabirds and marine mammals. This international database mostly includes data from the North Sea, yet large parts of the northeastern Atlantic Ocean are covered as well. It finds its origin in the 'Seabirds at Sea' project, which was initiated in 1979 following the discovery of major oil potential in the North Sea and an urgent need to gain more knowledge on the occurrence and distribution of seabirds in their offshore habitat. This led to the execution of large-scale ship-based surveys across the North Sea using a standardized data collection method and a first European-wide data assembly in 1991. ESAS data are collected by various partners during aerial or ship-based surveys at sea and according to a methodology that allows to calculate georeferenced seabird densities. Standard practice further implies collecting as much information as possible on animal age, plumage and behaviour as well as observation conditions and distance to the observed individuals. As part of the WOZEP research project, ESAS data were migrated in 2022 from its former host JNCC (UK) to ICES. The ICES infrastructure allows partners to submit new data and users to download or request data.
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Additional file 1: Figure S1. Whole-head serial sectioning and staining for FoxG1. All coronal paraffin sections ordered from ventral to dorsal. The dark anterior pigment corresponds to the frontal eye (FE). Apart from the expression in the brain, FoxG1 is also expressed in some cells of the floor plate (FP) and some ventrolateral cells of the central canal. We also observed expression in somites (M), as described previously by Toresson et al., 1998. Abbreviations: CC: Central Canal; FP: Floor plate; FE: Frontal eye; IO: Infundibular organ; M: Muscle; N: Notochord; NP: Neuropore.
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CzIPMR code to estimate the recovery time for Cystoseira zosteroides populations after a major disturbance at different temperature scenarios treatments. In addition, stochastic population growth rate (λs) and quasi-extinction probability at increasing frequency of two major disturbances at increasing temperature scenarios. These analyses correspond to the figures 4 and 5 of Capdevila et al. 2018 JEcol.MixedEffectsparamsParameter values needed for the Integral Projection Models used to model the life cycle and population dynamics of Cystoseira zosteroides. This includes seven demographic processes: 1.survival (σ), 2.growth (γ), 3.fertility (φ), 4.recruits per capita (δ(N)), 5.probability of settlement of recruits (ε), 6.early survival of recruits (σs) and 7.recruits size probability distribution.IPMFunctionsFunctions required to run the CzIPM.R script. This script contains the description of the growth, survival and fecundity functions used to build the IPMs.1. The best-fitted model for survival (σ) was a logistic mixed effect model including size as fixed factors and population nested in years as a random factor. 2. For growth (γ), the best-fitted model was a linear mixed effect model, with size as fixed factor and population nested in year as random factor. 3. Fertility (φ(z)), was estimated as the relation between reproductive status (reproductive vs. non-reproductive) and size with a binomial regression. 4. Recruitment per capita (δ(N)) is density-dependent in C. zosteroides (Capdevila et al., 2015), so a generalized linear model with Poisson error distribution and a log-link function was fitted, correlating the recruit:adult ratio as a function of the adult density. 5. To model the effect of temperature on the probability of settlement (ε) we used a generalized linear mixed models (GLMM), with a Poisson error distribution and a logit link function, the independent variable was the number of zygotes, temperature was treated as a fixed variable and we used the ID of each quadrat of the Petri dishes as a random variable. 6. To model the effect of temperature and time (fixed factors) on germling survival (σs), we used a GLMM with a binomial error distribution and a logit link function, with the ID of each quadrat of each Petri dish as a random variable to deal with the lack of independence between observations repeated at different times and a binomial error distribution was assumed to deal with the binary response variable (survive vs. die). 7. The size distribution of recruits was estimated as a normal probability function. In addition, the function required to project the density-dependent and stochastic IPMs is provided.modsumDensity-dependent function, relating the number of Cystoseira zosteroides recruits with the number of adults. It is a generalized linear model (GLM) with Poisson error distribution and a log-link function, correlating the recruit:adult ratio with the adult density. This file is needed to run the code CzIPM.R.settData on the impacts of temperature (16ºC, 20ºC and 24ºC) on the settlement of Cystoseira zosteroides early stages. This file is needed to perform the projections in CzIPM.R code.survrecData on the impacts of the temperature treatments (16ºC, 20ºC and 24ºC) to early survival of Cystoseira zosteroides. This file is required to run the code CzIPM.R. 1. Understanding the combined effects of global and local stressors is crucial for conservation and management, yet challenging due to the different scales at which these stressors operate. Here we examine the effects of one of the most pervasive threats to marine biodiversity, ocean warming, on the early life stages of the habitat-forming macroalga Cystoseira zosteroides, its long-term consequences for population resilience and its combined effect with physical stressors. 2. First, we performed a controlled laboratory experiment exploring the impacts of warming on early life stages. Settlement and survival of germlings were measured at 16ºC (control), 20ºC and 24ºC and both processes were affected by increased temperatures. Then, we integrated this information into stochastic, density-dependent integral projection models (IPM). 3. Recovery time after a minor disturbance significantly increased in warmer scenarios. The stochastic population growth rate (λs) was not strongly affected by warming alone, as high adult survival compensated for thermal-induced recruitment failure. Nevertheless, warming coupled with recurrent physical disturbances had a strong impact on λs and population viability. 4. Synthesis: The impact of warming effects on early stages may significantly decrease the natural ability of habitat-forming algae to rebound after major disturbances. These findings highlight that, in a global warming context, populations of deep-water macroalgae will become more vulnerable to further disturbances, and stress the need to incorporate abiotic interactions into demographic models.
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Pressione media al suolo (Pa). Corsa del 2024-01-01 ore 12 UTC - Valido dalle ore 12 UTC del 2024-01-01 alle ore 00 UTC del 2024-01-05. Modello meteorologico WRF (Weather Research and Forecasting model), core ARW (versione 3.2) con risoluzione spaziale a 3km, risoluzione temporale 60 ore, intervallo 1 ora. Средно налягане на земята (Pa). 2024—01—01 12 UTC — валиден от 2024—01—01 12 UTC до 2024—01—05 00 UTC. Метеорологичен модел WRF (модел за изследване и прогнозиране на Weather), ARW ядро (версия 3.2) с пространствена разделителна способност при 3 km, времева разделителна способност 60 часа, интервал 1 час. Vidējais zemes spiediens (Pa). 2024-01-01 12 UTC - spēkā no 2024-01-01 12 UTC līdz 2024-01-05 00 UTC. WRF meteoroloģiskais modelis (laika apstākļu izpētes un prognozēšanas modelis), ARW kodols (3.2. versija) ar telpisko izšķirtspēju 3 km attālumā, pagaidu izšķirtspēju 60 stundas, intervālu 1 stunda. Pressjoni medja tal-art (Pa). 2024-01-01 12 UTC - Validu mill-2024-01-01 12 UTC sal-2024-01-05 00 UTC. Mudell meteoroloġiku tad-WRF (Mudell ta’ Riċerka u Tbassir tat-Temp), qalba tal-ARW (verżjoni 3.2) b’riżoluzzjoni spazjali ta’ 3 km, riżoluzzjoni temporali ta’ 60 siegħa, intervall ta’ siegħa. Vidutinis žemės slėgis (Pa). 2024-01-01 12 UTC - Galioja nuo 2024-01-01 12 UTC iki 2024-01-05 00 UTC. WRF meteorologinis modelis (orų tyrimų ir prognozavimo modelis), ARW šerdis (3.2 versija), kurios erdvinė skiriamoji geba yra 3 km, laiko skiriamoji geba – 60 valandų, intervalas – 1 val. Presiunea medie la sol (Pa). 2024-01-01 12 UTC - Valabil de la 2024-01-01 12 UTC până la 2024-01-05 00 UTC. Modelul meteorologic WRF (modelul de cercetare și prognoză meteorologică), nucleul ARW (versiunea 3.2) cu rezoluție spațială la 3 km, rezoluție temporală 60 de ore, interval 1 oră. Durchschnittlicher Bodendruck (Pa). 2024-01-01 12 UTC - Gültig von 2024-01-01 12 UTC bis 2024-01-05 00 UTC. WRF-Meteorologisches Modell (Wetterforschungs- und Prognosemodell), ARW-Kern (Version 3.2) mit räumlicher Auflösung bei 3 km, zeitlicher Auflösung 60 Stunden, Intervall 1 Stunde. Średnie ciśnienie gruntu (Pa). 2024-01-01 12 UTC - Ważny od 2024-01-01 12 UTC do 2024-01-05 00 UTC. Model meteorologiczny WRF (Weather Research and Forecasting model), rdzeń ARW (wersja 3.2) z rozdzielczością przestrzenną na 3 km, rozdzielczość czasową 60 godzin, interwał 1 godzina. Povprečni tlak na tleh (Pa). 2024-01-01 12 UTC – velja od 2024-01-01 12 UTC do 2024-01-05 00 UTC. Meteorološki model WRF (model vremenskih raziskav in napovedi), jedro aluminijastih koles (različica 3.2) s prostorsko ločljivostjo 3 km, časovno ločljivostjo 60 ur, intervalom 1 ure. Presión media sobre el suelo (Pa). 2024-01-01 12 UTC - Válido desde 2024-01-01 12 UTC hasta 2024-01-05 00 UTC. Modelo meteorológico WRF (Weather Research and Forecasting model), núcleo ARW (versión 3.2) con resolución espacial a 3km, resolución temporal 60 horas, intervalo 1 hora.
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Raw data acquired by a JAVAD Delta 3 GNSS Receiver with a resolution of 50Hz on board RV Polarstern during the MOSAiC expedition.The data is stored in JAVAD's .jps format (JAVAD GNSS, GREIS – GNSS Receiver External Interface Specification, San Jose, USA, 2022 (download available at https://www.javad.com/jgnss/support/manuals.html)). Each file contains data of one day with a typical file size of 1GB. The receiver was equipped with a multi-frequency GNSS antenna which was mounted on the ship's observation deck. It has to be noted that the main mast and the ship's chimney lead to a shadowing of GNSS observation links in at least two directions seen from the antenna position. The data was collected for measuring scintillation activitiy in the central arctic. Processed scintillation measurements with a 1 minute resolution are available (doi:10.1594/PANGAEA.956019).
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doi: 10.17882/54520
WET Labs investigated the bias found in Poteau et al. 2017: http://dx.doi.org/10.1002/2017gl073949 and provides a matrix of affected sensors with scale factors for the backscattering channels using a correct weighted phase function constant values for ECO sensors mounted on BGC-Argo floats.
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From 1983 until 1989 NOAA-NCEI compiled the NOAA-MMS Marine Minerals Geochemical Database from journal articles, technical reports and unpublished sources from other institutions. At the time it was the most extended data compilation on ferromanganese deposits world wide. Initially published in a proprietary format incompatible with present day standards it was jointly decided by AWI and NOAA to transcribe this legacy data into PANGAEA. This transfer is augmented by a careful checking of the original sources when available and the encoding of ancillary information (sample description, method of analysis...) not present in the NOAA-MMS database.This dataset represents the digitized Table 1, pp. 68, of the related publication. During a short geological cruise in May 1979 by HMAS Kimbla, two manganese nodules were recovered from the deep sea about 250 nautical miles southeast of Sydney. They were laying on a greenish gray calcareous mud. The manganese nodules are subspherical with a rather irregular and rough surface, and are about 10 em in diameter. They consist of numerous concentric shells, many less than 0.1 mm thick, of brown and black metal oxides, and pale yellowish clay, in roughly equal proportions. The metal contents of the nodules (dried at 105°C) were determined at the Australia Bureau of Mineral Resources, Geology and Geophysics (BMR) using the atomic absorption method for Mn, Ni, Cu and Co, and a volumetric method for Fe.
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Ce jeu de données provient des analyses d'échantillons photos issus des déploiements de systèmes de caméras photo déposés (CPD) effectués lors de divers relevés en milieux côtiers sur la rive nord de l'estuaire et du golfe du Saint-Laurent entre Portneuf-sur-Mer et Sept-Îles, entre juin et octobre, de 2019 à 2022. Il contient les données de 4866 occurrences de 109 taxons d'invertébrés épibenthiques et de végétation aquatique submergée (y compris les algues) observés à des profondeurs allant de 0 à plus de 50 mètres. Des renseignements additionnels concernant ce jeu de données sont disponibles dans la section « Description des étapes méthodologiques ». Les relevés scientifiques ont été réalisés dans le cadre du Programme sur les données environnementales côtières de référence de Pêches et Océans Canada et du Plan de protection des océans. Cette initiative vise à acquérir des données environnementales de base qui contribuent à la caractérisation des zones côtières d'importance en soutient aux évaluations fondées sur des preuves ainsi que la prise de décisions de gestion afin de préserver les écosystèmes marins. Les données acquises lors des relevés comprennent aussi : 1) les données d'occurrence des taxons de poissons et invertébrés observés dans des échantillons vidéo provenant de systèmes de caméras vidéo stéréoscopiques appâtés (CVSA), 2) les données de capture de poissons et invertébrés dans un chalut à perche (occurrence et poids des captures des différents taxons), 3) la classification du substrat benthique basée sur les déploiements du système de caméras photos déposé, 4) des mesures océanographiques de la colonne d'eau d'un CTD Seabird 19plus V2 type profilage (conductivité, température, profondeur, rayonnement photosynthétique actif, pH, oxygène dissous), 5) les concentrations de nutriments (NO2, NO3, NH4, PO4, SiO3) et carbone organique dissous (DOC) et 6) la vitesse et la direction du courant mesurées par des inclinomètres. Les jeux de données des deux premiers éléments seront également disponibles en tant que jeux de données indépendants sur le portail OBIS/GBIF. Pour obtenir les données des éléments 3 à 6 et/ou les données biologiques récoltées sur différents taxons de poissons et invertébrés, veuillez contacter David Lévesque ou Marie-Julie Roux. L'élaboration d'objectifs de conservation écosystémiques dans la gestion des ressources halieutiques nécessite le développement de méthodes d'échantillonnage permettant de maximiser la collecte de données sur l'écosystème, tout en minimisant l'impact sur les organismes et le milieu marin. Ce projet vise la caractérisation écosystémique de la zone côtière de l'estuaire et du golfe du Saint-Laurent entre Portneuf-sur-Mer et Sept-Îles (QC), incluant la physico-chimie de l'eau, le phytoplancton, le zooplancton, la végétation submergée, les habitats benthiques ainsi que les assemblages de poissons et invertébrés. L'échantillonnage est réalisé en combinant des méthodes conventionnelles telles que le profilage CTD, les filets à zooplancton et le chalut à perche, à des méthodes non-extractives telles les caméras photo déposées (CPD) et les systèmes de caméras vidéo stéréoscopiques appâtés (CVSA). Les données amassées contribueront à définir les conditions écosystémiques de référence dans la zone d'étude; explorer les liens entre les conditions environnementales, la structure des habitats et les assemblages biologiques; identifier des habitats d'importance pour les espèces marines; ainsi qu'à l'évaluation de la performance des méthodes d'échantillonnage visuel par rapport aux méthodes conventionnelles. Les résultats permettront d'optimiser les suivis saisonniers ou annuels en vue de mieux comprendre les effets directs et indirectes des activités humaines en milieux côtiers. Description des étapes méthodologiques: 1. Acquisition des échantillons de photos en séquence : Le système de caméra photo déposé (CPD) utilisé pour échantillonner les images sous-marines est un cadre d'acier inoxydable ayant la forme d'un prisme à base triangulaire de 50 cm de largeur, de 100 cm de longueur et de 76 cm de hauteur au niveau de l'œillet central. La superficie du quadrat d'échantillonnage est de 0.25 m2 (dimensions intérieures de 50 cm par 50 cm). Le système est composé de deux caméras GoPro Hero 5 (4000 × 3000 pixels) et de deux lumières de plongée de 8000 lumens (Big Blue VL8000). La première caméra permet de capter les éléments se trouvant dans le quadrat en vue du dessus. La seconde caméra permet d'avoir un plan oblique facilitant l'évaluation des éléments présents dans le quadrat. À toutes les stations d'échantillonnage, cinq à neuf déploiements du système (réplicas) capturant des photos toutes les 10 secondes durant 60 à 120 secondes, ont été réalisés. 2. Analyse d'images: Une méthode d'analyse des images photo avec séquence (en mouvement) a été utilisée pour l'extraction des données d'occurrence et d'abondance des organismes; des mesures ont été prises pour obtenir les pourcentages de couverture de la végétation et des analyses du substrat ont également été effectuées. Les analyses ont été réalisées avec le logiciel ouvert Fiji de ImageJ. Une cote de qualité/visibilité a été attribuée aux séquences d'images analysées. 3. Approche taxonomique : Les organismes épibenthiques ont été identifiés au plus bas rang taxonomique possible. Une approche par morphotypes a systématiquement été utilisé (lors des annotations) pour l'identification des éponges, des hydrozoaires et des bryozoaires, et occasionnellement pour d'autres organismes tels que les algues. Des codes d'espèce ont également été utilisés pour distinguer certaines espèces qui ne pouvaient être identifiées au moment des annotations (voir verbatimIdentification). Pour éliminer le biais d'observateur, la même personne a analysé toutes les images utilisées dans cette base de données. Les organismes ont été identifiés à partir d'images sous-marines en utilisant une combinaison de guides d'identification et d'articles scientifiques. 4. Nomenclature ouverte : Le concept de nomenclature ouverte a été intégré dans les données d'occurrence pour accompagner les identifications taxonomiques avec leur niveau de certitude, tel que recommandé par Horton et al., 2021. L'abréviation stet. (stetit) a été utilisée lorsque la décision de ne pas aller plus bas a été prise mais qu'une identification est peut-être possible, alors que celle indet (Indeterminabilis) a été utilisé lorsqu'une identification plus bas niveau était considérée incertaine ou impossible (voir identificationqualifier). De plus, l'abréviation Confer (cf.) a été utilisée et intégrée dans les tables de données (voir occurenceRemarks) afin de relier des identifications qui pourraient potentiellement et/ou éventuellement être associées. 5. Remarques : Plusieurs remarques ont également été intégrées (voir organismRemarks, identificationRemarks et taxonRemarks), et visent à fournir des informations supplémentaires pouvant être utiles à certains utilisateurs des données; à noter que ces sections pourraient faire l'objet de modifications ou de bonification. 6. Contrôle qualité : Les identifications taxonomiques ont été vérifiés grâce à un processus de validation, en collaboration avec différents experts taxonomistes. Tous les noms scientifiques ont été vérifiés sur le registre mondial des espèces marines (WoRMS) pour correspondre aux normes actuellement reconnues. La correspondance WoRMS a été placée dans le champ taxonID du fichier d'occurrence. Le contrôle de la qualité des données a été effectué à l'aide des packages R obistools et worms. Tous les emplacements d'échantillonnage ont été reportés sur une carte afin d'effectuer un contrôle visuel confirmant que les coordonnées de latitude et de longitude se trouvaient dans la zone d'échantillonnage décrite. 7. Partage des données : Seules les métadonnées et les données d'occurrence de la biodiversité sont partagés dans ce jeu de données. Les deux fichiers fournis (format DarwinCore) sont complémentaires et sont liés par la clé « eventID ». Le fichier «event» comprend les informations génériques de l'activité, notamment la date et la localisation. Le fichier «occurrence» comprend les identifiants originaux des organismes observés, des commentaires d'identification et leur taxonomie. Un dictionnaire des données est aussi fournis pour expliquer les champs utilisés. Pour l'accès aux autres données ou aux images, contacter David Lévesque. Pour plus de détails à propos du projet et de la méthodologie, un rapport technique (Scallon-Chouinard et al., 2022) incluant les méthodes d'échantillonnage avec les systèmes de caméra déposé (CPD) et de caméras vidéo stéréoscopiques appâtés (CVSA), est actuellement disponible en ligne (https://waves-vagues.dfo-mpo.gc.ca/library-bibliotheque/41081171.pdf); un autre rapport technique détaillant les méthodes d'analyse d'images photo et vidéo sera également disponible. Ce projet a été financé par le Programme sur les données environnementales côtières de référence de Pêches et Océans Canada dans le cadre du Plan de protection des océans. This dataset is derived from analyses of photo samples obtained by deploying drop camera photo (DCP) systems conducted during various research surveys in coastal areas of the north shore of the St. Lawrence Estuary and the Gulf between Portneuf-sur-Mer and Sept-Îles between June and October of 2019 to 2022. It contains 4866 species occurrence data of 109 different taxa for epibenthic invertebrates and submerged aquatic vegetation (including algae) at depths ranging from 0 to more than 50 meters. Additional information about this dataset is available in the "Method step description" section. The research surveys were undertaken by the Department of Fisheries and Oceans Canada as part of the baseline program of the Ocean Protection Plan. This initiative aims to acquire environmental baseline data contributing to the characterization of important coastal areas and to support evidence-based assessments and management decisions for preserving marine ecosystems. Data acquired during the research surveys additionally include: 1) fish and invertebrate species occurrence data derived from analyses of video samples collected using a stereoscopic baited remote underwater camera video systems (stereo-BRUVs) 2) fish and invertebrates catch data from beam trawl sampling (occurrence and catch weights by species), 3) substrate classification based on drop camera samples, 4) oceanographic measurements of the water column from Seabird 19plus V2 profiling CTD (conductivity, temperature, depth, photosynthetic active radiation, pH, dissolved oxygen), 5) nutrients (NO2, NO3, NH4, PO4, SiO3) and dissolve organic carbon (DOC) concentrations, and 6) current speed and direction from tilt meters. The datasets of the first two elements will also be available as independent datasets on the OBIS/GBIF portal. To obtain data from items 3-6 and/or biological data collected on fish and invertebrate taxa, please contact David Lévesque or Marie-Julie Roux. The elaboration of conservation objectives based on an ecosystem assessment approach for fishery stock assessment requires the development of sampling methods to maximize the data collection on the ecosystem, while minimizing the impact on organisms and the marine environment. This project aims at characterising the coastal ecosystem of the St. Lawrence Estuary and Gulf between Portneuf-sur-Mer and Sept-Îles (QC), including the physico-chemistry of water, phytoplankton, zooplankton, submerged vegetation, benthic habitats as well as assemblages of fish and invertebrates. Sampling was performed by combining conventional methods such as CTD profiling, zooplankton nets, and beam trawl, with non-extractive methods such as drop camera photo (DCP) and stereoscopic baited remote underwater camera video systems (stereo-BRUVs). The data collected will help define baseline ecosystem conditions in the study area; explore the links between environmental conditions, habitat structure and biological assemblages; identify important habitats for marine species; as well as the evaluation of the performance of visual sampling methods compared to conventional methods. The results will make it possible to optimize the seasonal or annual monitoring in order to better understand the direct and indirect effects of human activities in coastal environments. Method Step Description: 1. Acquisition of photo samples in sequence: The drop camera photo (DCP) system used to sample underwater pictures is a stainless steel frame in the shape of a triangular prism of 50 cm wide, 100 cm long and 76 cm high at the level of the central eyelet. The sampling area is a quadrat of 0.25 m2 (interior dimensions of 50 cm by 50 cm). The system consists of two GoPro Hero 5 cameras (4000 × 3000 pixels) and two 8000 lumens dive lights (Big Blue VL8000). The first camera captures the elements located in the quadrat when viewed from above. The second camera offers an oblique view facilitating the evaluation of the elements present in the quadrat. At all sampling stations, five to nine system deployments (replicas) capturing photos every 10 seconds for 60 to 120 seconds were performed. 2. Image analysis: A photo image analysis method with sequence (moving images) was used for the occurrence data extraction and organism counts; measurements were taken to obtain vegetation cover percentages and substrate analyzes were also carried out. Analyzes were performed with the open-source Fiji software from ImageJ. A quality/visibility rating was assigned to the analyzed image sequences. 3. Taxonomic approach: Epibenthic organisms were identified at the lowest possible taxonomic rank. A morphotype approach has been systematically used (during annotations) for the identification of sponges, hydrozoans and bryozoans, and occasionally for other organisms such as algae. Species codes were also used to distinguish certain species that could not be identified at the time of the annotations (see verbatim Identification). To eliminate observer bias, the same person analyzed all images used in this database. The organisms were identified from underwater images using a combination of identification guides and scientific papers. 4. Open nomenclature: The concept of open nomenclature has been integrated into occurrence data to support taxonomic identifications with their level of certainty, as recommended by Horton et al., 2021. The abbreviation stet. (stetit) was used when the decision not to go lower was made but an identification might be possible, whereas indet (Indeterminabilis) was used when a lower level identification was considered uncertain or impossible (see identificationqualifier). In addition, the abbreviation Confer (cf.) was used and integrated into the data tables (see occurrenceRemarks) in order to link identifications that could potentially and/or possibly be associated. 5. Remarks: Several remarks have also been incorporated (see organismRemarks, identificationRemarks and taxonRemarks), and are intended to provide additional information that may be useful to some data users; Please note that these sections could be modified or improved. 6. Quality control: The taxonomic identifications were verified through a validation process, in collaboration with various expert taxonomists. All scientific names have been checked against the World Register of Marine Species (WoRMS) to match currently recognized standards. The WoRMS match was placed in the taxonID field of the instance file. Data quality control was performed using Robistools and worms packages. All sample locations were plotted on a map for visual verification that the latitude and longitude coordinates were within the described sample area. 7. Data sharing: Only metadata and biodiversity occurrence data are shared in this dataset. The two files provided (DarwinCore format) are complementary and are linked by the "eventID" key. The "event" file includes generic event information, including date and location. The "occurrence" file includes the original identifiers of the observed organisms, identification comments and their taxonomy. A data dictionary is also provided to explain the fields used. For access to other data or images, contact David Lévesque. For more details about the project and the methodology, a technical report (Scallon-Chouinard et al., 2022) including sampling methods with drop camera photo systems (DCP) and stereoscopic baited remote underwater camera video systems (stereo-BRUVs) is currently available online (https://waves-vagues.dfo-mpo.gc.ca/library-bibliotheque/41081225.pdf); another technical report detailing photo and video image analysis methods will also be available. This project is part of the Coastal Environmental Baseline Program under the Oceans Protection Plan of Fisheries and Oceans Canada.
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Aim: The interdependencies between trophic interactions, environmental factors and anthropogenic forcing determine how species distributions change over time. Large changes in species distributions have occurred as a result of climate change. The objective of this study was to analyse how the spatial distribution of cod and flounder have changed in the Baltic Sea during the past four decades characterized by large hydrological changes. Location: Baltic Sea Taxon: Cod (Gadus morhua) and flounder (Platichthys flesus) Methods: Catch per unit of effort (CPUE) data for adult and juvenile cod and for adult flounder were modelled using Delta-Generalized additive models including environmental and geographical variables between 1979 and 2016. From the annual CPUE predictions for each species, yearly distribution maps and depth distribution curves were obtained. Mean depth and the depth range were estimated to provide an indication on preferred depth and habitat occupancy. Results: Adult and juvenile cod showed a contraction in their distribution in the southern areas of the Baltic Sea. Flounder, instead, showed an expansion in its distribution with an increase in abundance in the northern areas. The depth distributions showed a progressive shift of the mean depth of occurrence towards shallower waters for adult cod and flounder and towards deeper waters for juvenile cod, as well as a contraction of the species depth ranges, evident mainly from the late 1980s. Main conclusions: Our study illustrates large changes in the spatial distribution of cod and flounder in the Baltic Sea. The changes in depth distribution occurred from the late 1980s are probably due to a combination of expanded areas of hypoxia in deep waters and an increase in predation risk in shallow waters. The net effect of these changes is an increased spatial overlap between life stages and species, which may amplify cod cannibalism and the interaction strength between cod and flounder. Data_cod_flounderAdult cod, juvenile cod and flounder CPUE data (in grams). The datasets contain also the associated bottom temperature, salinity and oxygen concentration of each haul as well as the latitude and longitude in decimal degrees.
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doi: 10.14284/601
European Seabirds At Sea (ESAS) assembles offshore monitoring data on seabirds and marine mammals. This international database mostly includes data from the North Sea, yet large parts of the northeastern Atlantic Ocean are covered as well. It finds its origin in the 'Seabirds at Sea' project, which was initiated in 1979 following the discovery of major oil potential in the North Sea and an urgent need to gain more knowledge on the occurrence and distribution of seabirds in their offshore habitat. This led to the execution of large-scale ship-based surveys across the North Sea using a standardized data collection method and a first European-wide data assembly in 1991. ESAS data are collected by various partners during aerial or ship-based surveys at sea and according to a methodology that allows to calculate georeferenced seabird densities. Standard practice further implies collecting as much information as possible on animal age, plumage and behaviour as well as observation conditions and distance to the observed individuals. As part of the WOZEP research project, ESAS data were migrated in 2022 from its former host JNCC (UK) to ICES. The ICES infrastructure allows partners to submit new data and users to download or request data.
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Additional file 1: Figure S1. Whole-head serial sectioning and staining for FoxG1. All coronal paraffin sections ordered from ventral to dorsal. The dark anterior pigment corresponds to the frontal eye (FE). Apart from the expression in the brain, FoxG1 is also expressed in some cells of the floor plate (FP) and some ventrolateral cells of the central canal. We also observed expression in somites (M), as described previously by Toresson et al., 1998. Abbreviations: CC: Central Canal; FP: Floor plate; FE: Frontal eye; IO: Infundibular organ; M: Muscle; N: Notochord; NP: Neuropore.
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CzIPMR code to estimate the recovery time for Cystoseira zosteroides populations after a major disturbance at different temperature scenarios treatments. In addition, stochastic population growth rate (λs) and quasi-extinction probability at increasing frequency of two major disturbances at increasing temperature scenarios. These analyses correspond to the figures 4 and 5 of Capdevila et al. 2018 JEcol.MixedEffectsparamsParameter values needed for the Integral Projection Models used to model the life cycle and population dynamics of Cystoseira zosteroides. This includes seven demographic processes: 1.survival (σ), 2.growth (γ), 3.fertility (φ), 4.recruits per capita (δ(N)), 5.probability of settlement of recruits (ε), 6.early survival of recruits (σs) and 7.recruits size probability distribution.IPMFunctionsFunctions required to run the CzIPM.R script. This script contains the description of the growth, survival and fecundity functions used to build the IPMs.1. The best-fitted model for survival (σ) was a logistic mixed effect model including size as fixed factors and population nested in years as a random factor. 2. For growth (γ), the best-fitted model was a linear mixed effect model, with size as fixed factor and population nested in year as random factor. 3. Fertility (φ(z)), was estimated as the relation between reproductive status (reproductive vs. non-reproductive) and size with a binomial regression. 4. Recruitment per capita (δ(N)) is density-dependent in C. zosteroides (Capdevila et al., 2015), so a generalized linear model with Poisson error distribution and a log-link function was fitted, correlating the recruit:adult ratio as a function of the adult density. 5. To model the effect of temperature on the probability of settlement (ε) we used a generalized linear mixed models (GLMM), with a Poisson error distribution and a logit link function, the independent variable was the number of zygotes, temperature was treated as a fixed variable and we used the ID of each quadrat of the Petri dishes as a random variable. 6. To model the effect of temperature and time (fixed factors) on germling survival (σs), we used a GLMM with a binomial error distribution and a logit link function, with the ID of each quadrat of each Petri dish as a random variable to deal with the lack of independence between observations repeated at different times and a binomial error distribution was assumed to deal with the binary response variable (survive vs. die). 7. The size distribution of recruits was estimated as a normal probability function. In addition, the function required to project the density-dependent and stochastic IPMs is provided.modsumDensity-dependent function, relating the number of Cystoseira zosteroides recruits with the number of adults. It is a generalized linear model (GLM) with Poisson error distribution and a log-link function, correlating the recruit:adult ratio with the adult density. This file is needed to run the code CzIPM.R.settData on the impacts of temperature (16ºC, 20ºC and 24ºC) on the settlement of Cystoseira zosteroides early stages. This file is needed to perform the projections in CzIPM.R code.survrecData on the impacts of the temperature treatments (16ºC, 20ºC and 24ºC) to early survival of Cystoseira zosteroides. This file is required to run the code CzIPM.R. 1. Understanding the combined effects of global and local stressors is crucial for conservation and management, yet challenging due to the different scales at which these stressors operate. Here we examine the effects of one of the most pervasive threats to marine biodiversity, ocean warming, on the early life stages of the habitat-forming macroalga Cystoseira zosteroides, its long-term consequences for population resilience and its combined effect with physical stressors. 2. First, we performed a controlled laboratory experiment exploring the impacts of warming on early life stages. Settlement and survival of germlings were measured at 16ºC (control), 20ºC and 24ºC and both processes were affected by increased temperatures. Then, we integrated this information into stochastic, density-dependent integral projection models (IPM). 3. Recovery time after a minor disturbance significantly increased in warmer scenarios. The stochastic population growth rate (λs) was not strongly affected by warming alone, as high adult survival compensated for thermal-induced recruitment failure. Nevertheless, warming coupled with recurrent physical disturbances had a strong impact on λs and population viability. 4. Synthesis: The impact of warming effects on early stages may significantly decrease the natural ability of habitat-forming algae to rebound after major disturbances. These findings highlight that, in a global warming context, populations of deep-water macroalgae will become more vulnerable to further disturbances, and stress the need to incorporate abiotic interactions into demographic models.
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